Since it hasn't been mentioned so far and it seems to be the right tool for exactly what you are trying to achieve: 
[Aggregate Polygons][1]

Set the **minimum_hole_size** to the minimum size of a polygon hole you want to keep. Smaller ones will be eliminated.

PS. The optional **minimum_area** value in the same tool does the same for the polygon parts that are not holes. 


 [1]: http://help.arcgis.com/EN/ArcGISDesktop/10.0/Help/index.html#//00700000000s000000